Capillary electrophoresis has been used for the enantiomeric resolution of several basic compounds of pharmaceutical interest employing a background electrolyte containing pepsin as chiral selector. The separations have been performed in a polyacrylamide-coated capillary to suppress or minimize the electroosmotic flow as well as the adsorption on the wall. The chiral selector filled only part of the capillary, moving in the opposite direction of analytes and keeping the detector cell free of the strong absorbing protein. The effect of pepsin concentration, pH, and concentration of the background electrolyte on resolution of enantiomers was studied. Enantiomeric resolution was achieved for trimipramine, propranolol, promethazine, verapamil, cloperastine, oxprenolol, and pindolol. © 1997 John Wiley & Sons, Inc. J Micro Sep9: 9–14, 1997